Systems and methods for an integrated bio-entity manipulation and processing semiconductor device

ABSTRACT

An integrated semiconductor device for manipulating and processing bio-entity samples is disclosed. The device includes a microfluidic channel that is coupled to fluidic control circuitry, a photosensor array coupled to sensor control circuitry, an optical component aligned with the photosensor array to manipulate a light signal before the light signal reaches the photosensor array, and a microfluidic grid coupled to the microfluidic channel and providing for transport of bio-entity sample droplets by electrowetting. The device further includes logic circuitry coupled to the fluidic control circuitry and the sensor control circuitry, with the fluidic control circuitry, the sensor control circuitry, and the logic circuitry being formed on a first substrate.

PRIORITY CLAIM AND CROSS-REFERENCE

This is a continuation-in-part of U.S. Ser. No. 13/716,709 filed on Dec.17, 2012, the entire disclosure of which is hereby incorporated byreference.

The present disclosure is related to the following commonly-assignedpatent applications, the entire disclosures of which are incorporatedherein by reference: U.S. patent application Ser. No. 13/830,234 filedon Mar. 14, 2013, entitled “OPTICAL DETECTION FOR BIO-ENTITIES”, andU.S. patent application Ser. No. 14/200,148 filed on Mar. 7, 2014,entitled “SEMICONDUCTOR ARRANGEMENT AND FORMATION THEREOF”.

BACKGROUND

Medical technology industries, including device manufactures as well aspharmaceuticals and biologics manufacturers, have experiencedsignificant commercial and technological growth over the past severaldecades. Since the discovery of DNA, our understanding of itsbio-informational role in the development, operation, and interaction ofpathogens and all living beings has significantly increased thanks tothe development of DNA sequencing techniques over the years. Throughimprovement in DNA sequencing detection techniques, scientists anddoctors have gained greater insight on diseases as well as moreeffective treatments for patients based on their genetic dispositions.Thus, the use and role of DNA sequencing results in health care hasincreased significantly.

DNA sequences are series of the nucleotide bases adenine, guanine,cytosine, and thymine, that dictate the formation of proteins inbiological systems. By analyzing a DNA sequence, important informationcan be gleaned for both diagnostic and therapeutic purposes.Additionally, the identification and quantification of other biologicalentities (bio-entities), such as proteins, small molecules, andpathogens has pushed forward the potential of medical knowledge tobenefit humankind.

There is currently a wide variety of bio-entity manipulation andprocessing techniques in use today that include the use of amplificationand labeling techniques within various methods that may allow foroptical detection. This may be done by using fluorescent dyes andexternal optical systems with analog-to-digital conversion systems toallow for the intensive computer processing required for handling thelarge amounts of data produced. However, many technical obstacles stillexist, such as controlling the fluid samples containing the bio-entityto be observed. Additionally, while the price of DNA sequencing hasfallen considerably since the Human Genome Project was completed,further cost savings are needed before the full power of DNA sequencingcan have an impact. Therefore, current bio-entity manipulation andprocessing technologies have not been completely satisfactory.

BRIEF DESCRIPTION OF THE DRAWINGS

Aspects of the present disclosure are best understood from the followingdetailed description when read with the accompanying figures. It isemphasized that, in accordance with the standard practice in theindustry, various features of the figures are not drawn to scale. Infact, the dimensions of the various features may be arbitrarilyincreased or decreased for clarity of discussion.

FIG. 1 is a cross-sectional diagram of an electrowetting-on-dielectricapparatus.

FIG. 2 is a cross-sectional diagram of a fluidic control system thatuses electrowetting to transport and manipulate bio-entity sampledroplets.

FIG. 3 is a diagram illustrating how certain actions may be achievedusing an electrowetting fluidic control system.

FIG. 4 is a diagram of a microfluidic grid for transporting and mixingtarget bio-entity samples and biological reagents.

FIG. 5 is a cross-sectional diagram of a lower substrate for use in abio-entity manipulation and processing system according to anembodiment.

FIG. 6 provides top views of three optical components that may be usedin a bio-entity manipulation and processing system according to anembodiment.

FIG. 7 is a cross-sectional diagram of an upper substrate that may beused in a bio-entity manipulation and processing system according to anembodiment.

FIG. 8 is a cross-sectional diagram of a microfluidic bio-entitymanipulation and processing system according to an embodiment.

FIG. 9 is a cross-sectional diagram of a microfluidic bio-entitymanipulation and processing system according to an additional embodimentthat includes a color filter array.

FIG. 10 is a cross-sectional diagram of a lower substrate of amicrofluidic bio-entity manipulation and processing system according toan embodiment that utilizes back-side exposure.

FIG. 11 is a flowchart of a method for manipulating and processingbio-entity samples with an integrated semiconductor device.

FIG. 12A is a top view illustrating a lower wafer in a microfluidicbio-entity manipulation and processing system according to someembodiments of the present disclosure.

FIG. 12B is a cross-sectional view of the lower wafer in a microfluidicbio-entity manipulation and processing system along the line A-A in FIG.12A according to some embodiments of the present disclosure.

FIG. 12C is a top view illustrating a lower wafer in a microfluidicbio-entity manipulation and processing system according to someembodiments of the present disclosure.

FIGS. 13A-13E are cross-sectional views of a lower wafer in amicrofluidic bio-entity manipulation and processing system fabricated atvarious steps according to some embodiments of the present disclosure.

FIG. 14 is a flowchart of a method for forming vertical electrodes in amicrofluidic bio-entity manipulation and processing system according tosome embodiments of the present disclosure.

FIG. 15A is a cross-sectional diagram of a microfluidic bio-entitymanipulation and processing system according to some embodiments of thepresent disclosure.

FIG. 15B is a cross-sectional diagram of an upper wafer that may be usedin a bio-entity manipulation and processing system according to someembodiments of the present disclosure.

FIG. 16 is an illustrative top view of an integrated device including amicrofluidic bio-entity manipulation and processing system according tosome embodiments of the present disclosure.

FIG. 17 is a flowchart of a method for manipulating and processingbio-entity samples with a microfluidic bio-entity manipulation andprocessing system according to some embodiments of the presentdisclosure.

The various features disclosed in the drawings briefly described abovewill become more apparent to one of skill in the art upon reading thedetailed description below.

DETAILED DESCRIPTION

It is to be understood that the following disclosure provides manydifferent embodiments and examples for implementing different featuresof the invention. Specific examples of components and arrangements aredescribed below to simplify the present disclosure. These are, ofcourse, merely examples and are not intended to be limiting. Moreover,the formation of a first feature over or on a second feature in thedescription that follows may include embodiments in which the first andsecond features are formed in direct contact, and may also includeembodiments in which additional features may be formed interposing thefirst and second features, such that the first and second features maynot be in direct contact. Various features in the figures may bearbitrarily drawn in different scales for the sake of simplicity andclarity. Where features depicted in the various figures are commonbetween two or more figures, the same identifying numerals have beenused for clarity of description. However, this should not be understoodas limiting such features.

FIG. 1 is a cross-sectional diagram of an electro-wetting-on-dielectric(EWOD) apparatus 100. The apparatus 100 includes a substrate 102 withthree material layers thereon. These material layers include anelectrode layer 104, a dielectric layer 106, and a hydrophobic coating108. The electrode layer 104 is coupled to a variable voltage source 110by a switch 112. Attached to the opposite end of the voltage source 110is a probe 114. As depicted in FIG. 1, the apparatus 100 positions theprobe 114 to be inserted into a droplet shown in two different states.Droplet 116A depicts the droplet in a state when no voltage is beingapplied by probe 114. Because of the hydrophobic coating 108, droplet116A has a contact angle θ₀ as shown. By applying a voltage from thevoltage source 110 through the probe 114, the contact angle can bedecreased and the contact area increased. Thus, droplet 116B is thedroplet when a voltage is applied. The contact angle is then decreasedto θ_(v), bringing the mass of the droplet 116B closer to the underlyingelectrode layer 104. The change in the contact angle caused by theapplied voltage is related to the applied voltage according to equation(1) below.

$\begin{matrix}{{{\cos\;\theta_{V}} - {\cos\;\theta_{0}}} = {\frac{{ɛɛ}_{o}}{2\gamma_{LG}t}V^{2}}} & (1)\end{matrix}$

In equation (1), V is the applied electrical potential or voltage, θ_(v)is the contact angle under applied voltage V, and θ₀ is the contactangle without applied voltage V. Other variables include: ε, thedielectric constant of the dielectric layer 106; ε₀, the vacuumpermittivity; γ_(LG), the surface tension; and t, the thickness ofdielectric layer 106. This manipulation of the apparent hydrophobicityof the droplet in apparatus 100 may be referred to aselectrowetting-on-dielectric (EWOD). Thus, by using EWOD, the physicalconfiguration of a droplet on a hydrophobic surface can be altered andcontrolled as seen in FIG. 1

FIG. 2 is a cross-sectional diagram of a fluidic control system 200 thatallows for transporting and manipulating bio-entity sample dropletsusing EWOD principles. The fluidic control system 200 operates around amicrofluidic channel 202 to control a droplet 204 within the channel.Droplet 204 is a bio-entity sample droplet. A “bio-entity” or“biological entity” as used herein may refer to DNA, RNA, a protein, asmall molecule, a virus or other pathogen, or any such thing that may besequenced, identified, or quantified. Such activities may take place ina medical or industrial context. Throughout the disclosure, the exampleof DNA sequencing is presented, however the embodiments are not limitedto this example.

As seen in FIG. 2, the bottom portion of the microfluidic channel 202 isprovided by a first substrate 206 with several layers thereon. Theselayers include three electrodes 208A, 208B, and 208C, which aresurrounded by a first dielectric layer 210. Above the dielectric layer210 is a first hydrophobic coating 212 that provides the lower surfaceof the microfluidic channel 202.

The top surface of the microfluidic channel 202 is provided by anotherhydrophobic coating, which is formed over a second substrate 214. Thissecond substrate 214 is a glass substrate upon which several materiallayers are deposited. These layers include a top electrode layer 216, asecond dielectric layer 218, and a second hydrophobic coating 220, whichforms the top surface of the microfluidic channel 202. The secondsubstrate 214 is inverted and brought close to the surface of the firsthydrophobic coating 212. Thus, the droplet 204 is physically bounded bythe first hydrophobic coating 212 on the bottom and the secondhydrophobic coating 220 on the top.

The bottom electrodes 208A, 208B, and 208C are coupled to a switch 222capable of selecting any combination of these three electrodes. Theswitch 222, in turn is connected to a voltage source 224, the oppositeside of which is connected to the top electrode layer 216. Byselectively applying a voltage to various combinations of electrodes208A, 208B, and 208C, the electric field in which the droplet 204 islocated can be altered. In the depicted embodiment a DC potential isapplied, but in other embodiments, an AC potential may be used instead.By controlling the electric fields between the bottom electrodes 208A,208B, and 208C and the top electrode 216, the droplet 204 itself can bemanipulated and transported in various ways. This can be betterunderstood by reference to FIG. 3.

FIG. 3 is a diagram illustrating how certain actions may be achievedusing an EWOD fluidic control system. Four exemplary actions aredepicted: a lateral movement 300A, a droplet split 300B, a dropletmerger 300C, and a droplet formation 300D. These examples depict actionsperformed in the fluidic control system 200 as seen from above, lookingdown onto the droplet 204 through substrate 214.

As depicted in the lateral movement 300A, the droplet 204 is situatedabove the electrode 208B. When switch 222 is asserted so that bottomelectrode 208A is disconnected from the voltage source 224 (OFF), bottomelectrode 208B is OFF, and bottom electrode 208C is connected to thevoltage source 224 (ON), the droplet moves in the direction of electrode208C until it is located over electrode 208C.

As depicted in the droplet split 300B, droplet 204 begins situated abovebottom electrode 208B. When switch 222 is asserted so that the bottomelectrode 208B is OFF and both bottom electrodes 208A and 208C are ON,the portion of the droplet 204 that is closest to bottom electrode 208Awill move to the left and the portion of the droplet 204 that is closestto bottom electrode 208C will move to the right, causing the droplet 204to be split into a droplet 204A situated over the bottom electrode 208Cand a droplet 204B situated over the bottom electrode 208A.

As depicted in the droplet merger 300C, the droplet 204 A beginssituated above 208C and the droplet 204B begins situated over 208A. Whenthe switch 222 is asserted so that bottom electrodes 208A and 208C areOFF and the bottom electrode 208B is ON, the droplets 204A and 204B bothmove toward the bottom electrode 208B. The droplets 204A and 204B willmerge over the bottom electrode 208B to form a single droplet.

A droplet formation 300D is also depicted in FIG. 3. Droplet formation300D depicts the formation of a bio-entity sample droplet from a largerbio-entity sample drop. The performance of droplet formation 300D usesthe three bottom electrodes 208A, 208B, and 208C, as discussed, andfurther includes a larger electrode 302. The larger electrode 302 mayallow for the placement of a larger volume of liquid in a drop 304. Inorder to form a droplet 204, all four electrodes (302, 208A, 208B, and208C) are turned ON to pull the drop 304 out along the path indicated bythe square bottom electrodes, then bottom electrodes 208B and 208C areturned OFF. The liquid over bottom electrodes 208B and 208C is pulledaway by the ON state of the other electrodes, and pushed away by thehydrophobicity of the bottom electrodes 208B and 208C in their OFFstate. The portion of drop 304 above 208A remains to form droplet 204.

These examples assume that any other adjacent electrodes are OFF. Thelateral movement 300A, the droplet split 300B, the droplet merger 300C,and the droplet formation 300D actions may be used to manipulate andtransport droplets as they move through the microfluidic channel 202 ofFIG. 2, and also through a microfluidic grid.

FIG. 4 is a diagram of a microfluidic grid 400 for transporting andmixing target bio-entities. For example microfluidic grid 400 may beused for transporting and mixing target DNA samples and biologicalreagents. The microfluidic grid includes a plurality of horizontal andvertical paths lined by electrodes like the electrodes 208A, 208B, and208C of FIG. 2. Actions like those described in connection with FIG. 3may be used to move, split, merge, and form droplets in the microfluidicgrid 400.

The plurality of vertical paths is labeled as vertical paths 402A-J,while the plurality of horizontal paths is labeled as horizontal paths404A-L. Each of vertical paths 402A-J and each of horizontal paths404A-L may be formed from a plurality of linearly arranged electrodes.The spaces in between the vertical paths 402A-J and the horizontal paths404A-L may be empty space as the hydrophobic coatings 212 and 220 mayeffectively bar a droplet from “jumping” from one hydrophilic path toanother with electrodes in an ON state. In some embodiments, materialbarriers exist in the spaces between the paths.

The microfluidic grid 400 also includes a plurality of tanks from whichdroplets are introduced into the plurality of paths. Arranged along thetop is a number of reagent tanks 406A-E. In the depicted embodiment ofmicrofluidic grid 400, these reagent tanks include an adenine reagenttank 406A, a thymine reagent tank 406B, a guanine reagent tank 406C, acytosine reagent tank 406D, and a buffer tank 406E. Other embodiments ofmicrofluidic grid 400 may include other biological reagents. Dropletsmay be dispensed into the microfluidic grid 400 through vertical paths402B, 402D, 402F, 402H, and 402J, and by selectively asserting theelectrodes that make up the horizontal and vertical paths, thesedroplets may be positioned any where in the microfluidic grid 400 anddivided and mixed, or merged, with other droplets. A number of reagentdroplets, including exemplary buffer droplet 408A and exemplary adeninereagent droplet 408B, are depicted along horizontal path 404C.

Depicted on the left-hand side of microfluidic grid 400 is a number ofbio-entity sample tanks 410A-D. In the depicted embodiment, used for DNAsequences, each bio-entity sample tank contains a different target DNAfragment, labeled as D1 in target DNA fragment tank 410A, D2 in targetDNA fragment tank 410B, D3 in target DNA fragment tank 410C, and D4 intarget DNA fragment tank 410D. In embodiments used for DNA sequencingthese tanks hold fragments of a DNA sample to be sequenced. Inembodiments used for diagnosis, other types of bio-entity samples, suchas antibodies, may be present in the sample tanks.

Sequencing the entire genome of a person or pathogen in a singlesequence would require a prohibitively long amount of time. Byfragmenting a DNA sample into many samples, each sample may be processedsimultaneously in order to decrease the total time required to obtainthe entire sequence. The fragments should be labeled beforehand so thatthe individual parallel sequencing can be recombined. Each square inFIG. 4 is a target DNA fragment, such as exemplary target DNA fragment410, that can be manipulated as described above in connection with FIG.3, including being mixed with a reagent droplet for tagging. The areaunderneath the microfluidic grid 400 includes a light sensor array,which may be used to take light-based measurements in order to sequencethe target DNA fragment samples. This may be better understood withreference to FIG. 5.

FIG. 5 is a cross-sectional diagram of a lower wafer 500 for use in amicrofluidic bio-entity manipulation and processing system. The lowerwafer 500 includes four main functional areas: a fluidic controlcircuitry area, a solid-state based photosensor array area, a logiccircuitry area, and a microfluidic channel area. The circuitry andphotosensor array areas are formed on or in a substrate 502. Asdepicted, substrate 502 is a silicon substrate. However, in otherembodiments, substrate 502 may be a substrate formed from anothersuitable elementary semiconductor, such as diamond or germanium; asuitable compound semiconductor, such as silicon carbide, indiumarsenide, or indium phosphide; or a suitable alloy semiconductor, suchas silicon germanium carbide, gallium arsenic phosphide, or galliumindium phosphide.

The fluidic control circuitry area includes fluidic control circuitry504, which includes a plurality of metallization layer connected withassociated transistors and other circuit components for programming thepath of droplet movement. The sensor array area includes a photosensorarray 506 and photosensor control circuitry 508. In the depictedembodiment, the photosensor array 506 is an array of transistor-basedphotosensors and is a CMOS image sensor array. However, in otherembodiments the photosensor array may include photodiodes, active pixelsensors, phototransistors, photoresistors, charged coupled devices, orthe like. The photosensor array 506 is controlled by the photosensorcontrol circuitry 508, which also includes a plurality of transistorsand other circuit components. Finally, in the logic circuitry area,there is a significant amount of logic circuitry 510, includingtransistors and other circuit components. The logic circuitry 510 allowsfor input to and output from the lower wafer 500. Further logiccircuitry 510 is coupled to both the photosensor control circuitry 508and the fluidic control circuitry 504, to provide both with signalprocessing for optimal operation, such as analog-to-digital anddigital-to-analog conversion. Fluidic control circuitry 502, photosensorcontrol circuitry 508, and logic circuitry 510 are embedded in aninter-metal dielectric layer (IMD) 512.

On top of the IMD 512, is a plurality of bottom electrodes, much likethe bottom electrodes of FIG. 2. Included in FIG. 5, three bottomelectrodes are depicted: bottom electrodes 514A, 514B, and 514C. Manymore electrodes may be present in practice, but the three depicted areadequate for clear discussion of lower wafer 500. In the depictedembodiment, bottom electrodes 514A, 514B, and 514C are made from analuminum-copper alloy. However, in other embodiments different materialsmay be used that are also suitable for electrodes. Bottom electrodes514A and 514C are solid rectangles as viewed from above, however thebottom electrode 514B is not. This will be discussed further withreference to FIG. 6. In FIG. 5, only the bottom electrode 514A appearsto be connected to the fluidic control circuitry metallization stack.However, all bottom electrodes 514A, 514B, and 514C are in communicationwith the fluidic control circuitry 504, and thus all may be in an ON orOFF state as described in connection with FIG. 3.

On top of and surrounding the sides of bottom electrodes 514A, 514B, and514C is a dielectric layer 516. In the depicted embodiment, dielectriclayer 516 is a high-k dielectric layer formed by an atomic layerdeposition (ALD) process, or a chemical vapor deposition (CVD) process,then followed by an annealing process. Over the dielectric layer 516 isa hydrophobic coating 518. In the depicted embodiment, hydrophobiccoating 518 is made from polytetrafluoroethylene (PTFE), while in otherembodiments it is a self-assembled monolayer. Also depicted in FIG. 5 isa contact pad 520 that is provided by etching through a portion of thehydrophobic coating 518, the dielectric layer 516, and a thickness ofIMD 512. Other embodiments may feature additional metal layers and othervariations, but in any embodiment, contact pad 520 may be provided toallow power or ground to be supplied to the lower wafer 500, or to allowfor signal/control input or output.

FIG. 6 provides top views of three variations of bottom electrode 514Bthat also serve as optical components that may be used in a bio-entitymanipulation and processing system. Thus, in the depicted embodiments,optical components 600A, 600B, and 600C are made from aluminum. Otherembodiments may be made from other materials. Optical component 600A isa rectangular grating, including a plurality of regular holes through arectangular plate. By controlling the proximity and dimensions of therectangular holes, optical component 600A may separate certainwavelength of light. This may aid in DNA sequencing because some tagsgenerate light at a specific, identifiable frequency when removed.Background noise may be decreased by use of optical component 600A asbottom electrode 514B.

Optical component 600B is a plurality of concentric rings, with regularspacing in between each ring. Using the optical component 600B or othersimilar component as the bottom electrode 514B may allow for theconcentration of light onto the sensor array. Additionally, opticalcomponent 600C may be used as the bottom electrode 514B. Opticalcomponent 600C may be a pass-through structure that simply allows lightto pass through naturally from above the lower wafer 500 down onto thephotosensor array 506. Optical component 600C may serve to limitoff-axis light from being detected by the photosensor array 506. Otheroptical components may be used as desired in order to provide opticalinterference, diffraction, grating, and spectrophotometric functions forbio-optical applications. Optical components 600A, 600B, and 600C arebut a few examples. Other embodiments may include a transparentconductor, such as an indium tin oxide (ITO), as the bottom electrode514B.

FIG. 7 is a cross-sectional diagram of an upper wafer 700 that may beused in a bio-entity manipulation and processing system. The upper wafer700 includes a substrate 702. In the depicted embodiment, substrate 702is a glass wafer. However, in other embodiments, substrate 702 may beone of the materials mentioned above in alternate embodiments ofsubstrate 502 of lower wafer 500 in FIG. 5. Over substrate 702 is a topelectrode 704. In the depicted embodiment, top electrode 704 is an ITOlayer. However, in other embodiments, top electrode 704 may be analuminum layer or another suitable electrode layer.

A dielectric layer 706 is deposited over the top electrode 704. In thisexample, the dielectric layer 706 is a high-k dielectric layer that hasbeen deposited by an ALD process before being annealed. Additionally, ontop of the dielectric layer 706 is a hydrophobic coating 708. In thedepicted embodiment, the hydrophobic coating 708 is made from PTFE, butin other embodiments the hydrophobic coating 708 is made from aself-assembling monolayer. A portion of the hydrophobic coating 708 hasbeen treated with a surface treatment for labeling target DNA fragments,to create a surface treated area 710. In the depicted embodiment, thesurface treated area 710 may promote DNA binding, while in otherembodiments, an antibody binding surface treatment may be applied. Thesurface treated area 710 allows identifiable reactions to take placethat give of light when a droplet containing components that react withthe particular surface treatment are brought into contact with thesurface treated area 710. For example, a molecular tag may be added ontobase pairs that combine with the target DNA fragment, releasing the tagupon combination, with the release of the tag emitting a light signal.

FIG. 7 also depicts a contact pad area 712. Contact pad area 712 may beformed simply by etching away a portion of the hydrophobic coating 708and the dielectric layer 706 so that electrical contact may be made withan exposed portion of the top electrode 704. In other embodiments,additional contacting layers may be deposited over the exposed portionof the top electrode 704 to facilitate wire bonding.

FIG. 8 is a cross-sectional diagram of an integrated microfluidicbio-entity manipulation and processing system 800 that integrates thelower wafer 500 of FIG. 5 and the upper wafer 700 of FIG. 7. Thus FIG. 8includes the substrate 502, with the fluidic control circuitry 504, thephotosensor control circuitry 508, and the logic circuitry 510 thereon,in addition to the photosensor array 506 therein. An IMD 512 surroundsthose features, and the integrated lower wafer 500 includes bottomelectrodes 514A, 514B, and 514C deposited thereon with an overlyingdielectric layer 516. On top of the dielectric layer 516 is ahydrophobic coating 518 that serves as the bottom of a microfluidicchannel 802.

The microfluidic bio-entity manipulation and processing system 800 alsoincludes substrate 702, which in this embodiment is a glass substrate.Over substrate 702 are a top electrode 704, a dielectric layer 706, anda hydrophobic coating 708. While the depicted embodiment of microfluidicbio-entity manipulation and processing system 700 does not depicted thecontact pad area 712 of FIG. 7, other embodiments may contain such afeature. The hydrophobic coating 708 includes a surface treated area710. The lower wafer 500 and upper wafer 700 are combined usingdie-level or wafer-level packaging techniques so that the surfacetreated area 710 is aligned with the photosensor array 506 and so thatthe hydrophobic coatings 518 and 708 are brought close together, withoutcontacting, to form the microfluidic channel 802. While in the depictedembodiment the surface treated area 710 is formed on hydrophobic coating708, in other embodiments surface treated area 710 may be formed onhydrophobic coating 518 of lower wafer 500 instead, which may improveperformance by bringing the surface treated area 710 closer tophotosensor array 506.

In operation, a droplet 804 is brought into contact with the surfacetreated area 710 using the actions depicted in FIG. 3, such as thelateral movement 300A. The droplet 804 includes a tagged bio-entitysample, such as DNA mixed with a reagent droplet such as the exemplaryadenine reagent droplet 408B from FIG. 4. When the droplet 804 contactsthe surface treated area 710, chemical reactions may remove the tag fromthe bio-entity samples in the droplet. The removal of the tag mayenhance or intensify a photonic emission. The emission passes throughthe bottom electrode 514B, which in this embodiment is in the form ofthe optical component 600A of FIG. 6, and then is sensed in thephotosensor array 506. This signal is captured by the photosensorcontrol circuitry 508, and transmitted to the logic circuitry 510 forsignal processing. Depending on the frequency or color of the photonicemission, a specific base pair may be detected. In embodiments, in whichantibodies in the droplet 804 are being tested, the emission mayindicate the presence of the particular antibody in the bio-entitysample in droplet 804. After the droplet 804 has been processed in thismanner, it may be moved out of the microfluidic channel 802, and may bemoved out of the microfluidic grid 400.

As seen in FIG. 8, the microfluidic bio-entity manipulation andprocessing system 800 provides microfluidic control circuitry 504 (withassociated bottom electrodes 514A, 514B, and 514C), logic circuitry 510,and photosensor array 506, and photosensor control circuitry 508, on asingle wafer, lower wafer 500. The lower wafer 500 also provides for abottom surface of a microfluidic channel 804. The upper wafer 700,bonded to the lower wafer 500, provides the top surface of themicrofluidic channel and the top electrode 704. In the depictedembodiment, with high-k dielectric layers 706 and 516, an electricpotential of about 5 volts may be used to move and manipulate dropletslike droplet 804, as well as power the various circuitry components forimage sensing and processing, all on a single chip package.

FIG. 9 is a cross-sectional diagram of an integrated microfluidicbio-entity manipulation and processing system 900 according to anadditional embodiment that includes a color filter array. Severalfeatures are common between the microfluidic bio-entity manipulation andprocessing system 900 and the microfluidic bio-entity manipulation andprocessing system 800 of FIG. 8. Such common features are commonlynumbered to avoid unnecessary repetition in this disclosure. Underneaththe bottom electrodes 514A, 514B, and 514C is a color filter array (CFA)902, with a plurality of red, blue, and green filters. As depicted inFIG. 9, the bottom electrode 514B is configured as the optical component600C of FIG. 6. Thus, when an emission is caused by the removal of tagfrom a bio-entity sample droplet 904 by a reaction at the surfacetreated area 710, the path passes through the opening of the bottomelectrode 514B, through the CFA 902 before entering the photosensorarray 506 where the emission can be detected. The addition of the CFA902 may allow for the more traditional methods of detecting the color ofemissions. By detecting the color of the emissions, the particular tagbeing removed by the reaction at the surface treated area 710 can beidentified. In this manner, DNA fragments may be sequenced and specificpathogens may be detected.

While in the depicted embodiment the surface treated area 710 is formedon hydrophobic coating 708 of upper wafer 700, in other embodimentssurface treated area 710 may be formed on hydrophobic coating 518 oflower wafer 500 instead, which may improve performance by bringing thesurface treated area 710 closer to photosensor array 506.

FIG. 10 is a cross-sectional diagram of an integrated microfluidicbio-entity manipulation and processing system 1000 according to anadditional embodiment that utilizes back-side illumination. The lowerwafer of system 1000 is fabricated on a substrate 1002. In the depictedembodiment, substrate 1002 is a P-type silicon substrate, but in otherembodiments it may be other materials as described above. Duringfabrication, a plurality of metal layers is deposited to form fluidiccontrol circuitry 1004, photosensor control circuitry 1006, and logiccircuitry 1008. A plurality of photodetectors are fabricated insubstrate 1002 to create a photosensor array 1010 that is incommunication with photosensor control circuitry 1006. After an IMD 1012has covered the control and logic circuitries, the material stack onsubstrate 1002 is bonded to a carrier wafer 1014. Carrier wafer 1014 isa silicon wafer in the depicted embodiment, but may be a glass or othermaterial wafer in other embodiments.

After bonding the carrier wafer 1014 to the top of IMD 1012, the bondedwafers are flipped, and the back side of the substrate 1002 is thinned.In the present embodiment, a high selectivity wet etching process usinghydrofluoric, nitric, and acetic acids (HNA) is used to thin substrate1002. In an alternative embodiment, a chemical mechanical planarization(CMP) process may be used to thin substrate 1002. After the thinningprocess the photodetectors in the photosensor array 1010 are close tothe back side surface of substrate 1002. This may decrease the overallstack height between the photosensor array 1010 and the source ofemissions, thereby improving performance.

An anti-reflective coating (ARC) 1016 is deposited and patterned on topof the back side of substrate 1002. In the depicted embodiment, ARC 1016may be a silicon oxide ARC layer. After the ARC 1016 is patterned aplurality of bottom electrodes may be deposited. FIG. 1000 depicts fourbottom electrodes: bottom electrodes 1018A, 1018B, 1018C, and 1018D. Inthe depicted embodiment, bottom electrodes 1018A and 1018C aretransparent bottom electrodes, made from ITO. Meanwhile, bottomelectrode 1018B and 1018D are back side metal electrodes made of analuminum-copper alloy. Other configurations and materials may be usedfor the bottom electrodes 1018A, 1018B, 1018C, and 1018D in otherembodiments. In embodiments where more than one material is used for thebottom electrodes, different processes will be used for deposition andpatterning. In general, a portion of the photosensor array 1010 iscovered by an opaque material, which in the depicted embodiment isprovided by bottom electrode 1018B. This opaque material is used as adark reference, to determine the amount of signal from the photosensor1010 that is attributable to sources other than visible light, such asheat.

A dielectric layer 1020 is deposited on top of the bottom electrodes, aswell as the exposed portions of ARC 1016 and the back side of substrate1002. In the depicted embodiment, the dielectric layer 1020 is a high-kdielectric layer, deposited by an ALD process and then annealed, whilein other embodiments dielectric layer 1020 is deposited by a CVD beforeannealing. Over the dielectric layer 1020, a hydrophobic coating 1022 isdeposited. Hydrophobic coating 1022 provides the bottom half of amicrofluidic channel 1024, through which a droplet 1026 may be moved. Inthe depicted embodiment, the hydrophobic coating 1022 is made from PTFE.In other embodiments, it may be a self-assembling monolayer. Alsodepicted in FIG. 10 is a contact pad 1028 formed by etching through thehydrophobic coating 1022, the dielectric layer 1020, through substrate1002 and a portion of IMD 1012. Contact pad 1028 provides a location forwire bonding to allow for input and output as well as a power supplyconnection to logic circuitry 1008 and other circuitry embedded in IMD1012.

The wafer based on lower substrate 1002 is bonded to an upper wafer,like upper wafer 700 of FIG. 7. Thus, the upper wafer 700 includes asubstrate 702, a top electrode 704, a dielectric layer 706, and ahydrophobic coating 708 with a surface treated area 710. Along with thehydrophobic coating 1022, hydrophobic coating 708 forms the microfluidicchannel 1024. As discussed with other embodiments herein, the droplet1026 can be moved into contact with the surface treated area 710, whichprovides a site for characteristic biochemical interactions withbio-entities that emit light. These light emissions are detected by thephotosensor array 1010 and then processed to determine the entitiesinvolved in the reaction. By determining these entities, a nucleotidebase or a specific antibody may be registered. While in the depictedembodiment the surface treated area 710 is formed on hydrophobic coating708, in other embodiments surface treated area 710 may be formed onhydrophobic coating 1022 of the wafer based on lower substrate 1002instead, which may improve performance by bringing the surface treatedarea 710 closer to photosensor array 1010.

FIG. 11 is a flowchart of a method 1100 for manipulating and processingbio-entity samples with an integrated semiconductor device. The method1100 begins in step 1102 when a bio-entity sample droplet is obtainedfrom a first reservoir. The first reservoir is coupled to a microfluidicgrid. The method 1100 may continue in step 1104 when the bio-entitysample droplet is transported from the microfluidic grid into amicrofluidic channel using an electrowetting effect. The microfluidicchannel has a side provided on a first substrate. When in themicrofluidic channel the bio-entity sample droplet contacts a surfacetreatment in the microfluidic channel. A biochemical reaction istriggered upon contact between the bio-entity sample droplet and thesurface treatment. In step 1106, a photonic signal that is produced bythe interaction of the bio-entity sample droplet and the surfacetreatment is detected by a photosensor array that is formed on the firstsubstrate.

To better illustrate method 1100 in operation, reference will be made tothe integrated microfluidic bio-entity manipulation and processingsystem 800 of FIG. 8 and some other figures discussed above such as FIG.3 and FIG. 4. Method 1100 may also be explained with reference to otherembodiments of integrated microfluidic bio-entity manipulation andprocessing systems disclosed here in. Thus, reference to FIG. 8 is madeby way of non-limiting example. A reservoir 410A of FIG. 4 may include alarger volume of a bio-entity sample. By using the action depicted asdroplet formation 300D of FIG. 3, a bio-entity sample droplet 804 isformed from the larger volume and introduced into the microfluidic grid400 of FIG. 4 (step 1102). The bio-entity sample droplet 804 istransported through microfluidic grid 400, which includes a plurality ofmicrofluidic channels, one of which is microfluidic channel 802 of FIG.8. Microfluidic channel 802 is located on top of a material stackdeposited on substrate 502, the top layer of which, hydrophobic coating518, supplies the bottom surface of the microfluidic channel 802.Transporting the bio-entity sample droplet 804 through the microfluidicchannel is accomplished by using the logic circuitry 510 to control thefluidic control circuitry 504.

The bio-entity sample droplet 804 is moved through the microfluidic grid400 of FIG. 4 and the microfluidic channel 802 of FIG. 8 by using theelectrowetting effect. Bottom electrodes 514A, 514B, and 514C areasserted in either ON or OFF states as indicated by FIG. 3, in order tosubject the biological droplet to controlled hydrophobic or hydrophilicsurfaces according to the ON or OFF states of the bottom electrodes. Bycontrol of the bottom electrodes 514A, 514B, and 514C, and inconjunction with a top electrode 704, the bio-entity sample droplet 804is guided into contact with the surface treated area 710, which has hada surface treatment applied to it (step 1104). Guiding the bio-entitysample droplet 804 into contact with the surface treated area 710 isaccomplished by having the logic circuitry 510 exert control over thefluidic control circuitry 504.

Because of the surface treatment, surface treated area 710 and thebio-entity sample droplet 804 may undergo a biochemical reaction whichintensifies or enhances the fluorescent light signal. This light passesthrough the bottom electrode 514B to a photosensor array 506.Photosensor 506 detects the light and a corresponding signal is sent tothe logic circuitry 510 for processing (step 1106). Logic circuitry 510may interpret the signal by color or frequency to determine thebiochemical reaction that occurred. The biochemical reaction mayindicate that a specific base nucleotide was detected in a target DNAfragment, or that a particular antibody was present in the bio-entitysample droplet. After the bio-entity sample droplet 804 has beenprocessed, it may be removed from the microfluidic channel 802. In someembodiments a buffer droplet, such as buffer droplet 408A of FIG. 4, maybe transported through the microfluidic channel 802 in order to cleanit.

Additionally, in some embodiments of method 1100, an adenine reagentdroplet 408B obtained from the adenine reagent tank 406A in FIG. 4 iscombined with the bio-entity sample droplet 804, using the droplet merge300C operation of FIG. 3. The droplet merge 300C operation may mix thebio-entity sample droplet 804 and the adenine reagent droplet 408B inthe microfluidic grid 400. The mixed bio-entity sample droplet 804 maythen be directed into contact with the surface treated area 710 in themicrofluidic channel 802. In some embodiments, bottom electrode 514B maybe an optical component in addition to acting as an electrode. Thus thebottom electrode 514B may be optical component 600A in one embodiment,and 600B in another embodiment. In other embodiments, a reagent otherthan the adenine reagent droplet 408B may be used to create a differentmixed bio-entity sample droplet 804.

One of the broader embodiments is an integrated semiconductor device formanipulating and processing bio-entity samples. The device may include amicrofluidic channel, the channel being coupled to fluidic controlcircuitry, and a photosensor array coupled to sensor control circuitry.The device may also include logic circuitry coupled to the fluidiccontrol circuitry and the sensor control circuitry. The fluidic controlcircuitry, the sensor control circuitry, and the logic circuitry may beformed on a front side of a first substrate.

Another of the broader embodiments is an integrated semiconductor devicefor manipulating and processing genetic samples. The integratedsemiconductor device may include a microfluidic channel, themicrofluidic channel being coupled to fluidic control circuitry. Thedevice may further include a photosensor array coupled to sensor controlcircuitry, an optical component aligned with the photosensor array tomanipulate a light signal before the light signal reaches thephotosensor array, and a microfluidic grid coupled to the microfluidicchannel and providing for transport of genetic sample droplets byelectrowetting. Additionally, the device may include logic circuitrycoupled to the fluidic control circuitry and the sensor controlcircuitry. The fluidic control circuitry, the sensor control circuitry,and the logic circuitry are formed on first substrate.

Yet another of the broader embodiments is a method for manipulating andprocessing bio-entity samples with an integrated semiconductor device.The method may include steps of providing a bio-entity sample dropletfrom a first reservoir, the first reservoir coupled to a microfluidicgrid; transporting the bio-entity sample droplet from the microfluidicgrid into a microfluidic channel using an electrowetting effect, anddetecting a photonic signal with a photosensor array. The bio-entitysample droplet may contact a surface treatment in the microfluidicchannel, wherein one side of the microfluidic channel is provided on afirst substrate. The photonic signal is enhanced by an interaction ofthe bio-entity sample droplet and the surface treatment, and thephotosensor array is formed on the first substrate.

FIG. 12A is a top view illustrating a lower wafer 1200 including one ormore vertical electrodes 1210 in a microfluidic bio-entity manipulationand processing system according to some embodiments. In someembodiments, the lower portion 1202 of the lower wafer 1200 may includea substrate, a photosensor array, one or more circuitries embedded in aninter-metal dielectric layer (IMD) as discussed with regard to FIG. 5.In some embodiments, each of the vertical electrodes has a length alongX-dimension in a range from about 50 μm to about 5000 μm. As shown inFIG. 12A, a channel gap (g) between the two adjacent vertical electrodesalong the Y-dimension is in a range from about 30 μm to about 1000 μm.

Still referring to FIG. 12A, a droplet 1220 is brought into contact withthe vertical electrodes 1212 and 1214, and a droplet 1222 is broughtinto contact with the vertical electrodes 1216 and 1218. The verticalelectrode 1212 is coupled to a voltage source 1240, and the voltagesource 1240 is coupled to a switch 1242 capable of selecting any statusbetween ON and OFF by connecting or disconnecting the switch 1242 to thevertical electrode 1214. Similarly, the vertical electrode 1216 iscoupled to a voltage source 1244, and the voltage source 1244 is coupledto a switch 1246 capable of selecting any status between ON and OFF byconnecting or disconnecting the switch 1246 to the vertical electrode1218. By selectively applying a voltage between vertical electrodes 1214and 1214, an electric field applied to the droplet 1220 can be altered,manipulated and transported in various ways. Similarly, by selectivelyapplying a voltage to vertical electrodes 1216 and 1218, an electricfield applied to the droplet 1222 can be altered, manipulated andtransported in various ways. In the depicted embodiment a DC potentialis applied, but in other embodiments, an AC potential may be usedinstead.

FIG. 12B is a cross-sectional view of the lower wafer 1200 including thevertical electrodes 1210 along the line A-A in FIG. 12A according tosome embodiments. As shown in FIG. 12B, the one or more electrodes onthe lower portion 1202 are vertical electrodes 1210, so that thedroplets 1220 and 1222 may be moved within the channel gap (g) betweentwo adjacent rows of the vertical electrodes. For example, the droplet1220 may be moved in a channel gap (g1) between the vertical electrode1212 and the vertical electrode 1214, and the droplet 1222 may be movedin a channel gap (g2) between the vertical electrode 1216 and thevertical electrode 1218. Each of the vertical electrodes has a height(h) along Z-dimension in a range from about 2 μm to about 100 μm. Thedroplet 1220 and/or the droplet 1222 may be substantially similar to thedroplet 804, which may include a tagged bio-entity sample.

In some embodiments, a dielectric layer 1232 may be formed on andconformed to the surface of each of the vertical electrodes 1210. Thedielectric layer 1232 may include a high-k dielectric material, and maybe deposited using an ALD process or a CVD process followed by anannealing process. A hydrophobic coating 1234 may be further formed onthe dielectric layer 1232, and the hydrophobic coating 1234 may also beconformed to the surface of each of the vertical electrodes 1210.Referring back to FIG. 12A, in some embodiments, the dielectric layer1232 and/or the hydrophobic coating 1234 formed on the adjacent verticalelectrodes may offer sufficient isolation between the two adjacentvertical electrodes along the X dimension; meanwhile, the dielectriclayer 1232 and/or the hydrophobic coating 1234 formed on the adjacentvertical electrodes may also prevent the droplets from diffusing intothe space between the vertical electrodes along the X-dimension.

FIG. 12C is a top view illustrating a lower wafer 1250 in a microfluidicbio-entity manipulation and processing system according to someembodiments of the present disclosure. The layout of the one or morevertical electrodes on the lower wafer 1250 may be designed to offerdifferent channels gaps for holding different droplet volumes. Forexample, the channel gap between the vertical electrode 1256 and thevertical electrode 1258 may be substantially greater than the channelgap (g3) between the vertical electrode 1252 and the vertical electrode1254. Therefore, the channel gap (g4) is able to hold a droplet 2 withgreater volume than a droplet 1 being held by the channel gap (g3). Thevarious embodiments of the vertical electrode design layout may offermore flexibility for testing the samples with different volumes usingthe microfluidic bio-entity manipulation and processing system asdiscussed in the present disclosure. The lower wafer 125 may alsoinclude one or more contact pads 1260 for supplying power or ground tothe lower wafer 1250, or for providing signal/control input or output.

FIGS. 13A-13E are cross-sectional views of a lower wafer 1300 in amicrofluidic bio-entity manipulation and processing system fabricated atvarious steps according to some embodiments. The lower wafer 1300 inFIGS. 13A-13E may be substantially similar to the lower wafer 1200 inFIGS. 12A-12B. Referring to FIG. 13A, the lower wafer 1300 includes asubstrate 1302. The substrate 1302 may include a silicon substrate. Insome alternative embodiments, the substrate 1302 may include any othersuitable elementary semiconductor, such as diamond or germanium; asuitable compound semiconductor, such as silicon carbide, indiumarsenide, or indium phosphide; or a suitable alloy semiconductor, suchas silicon germanium carbide, gallium arsenic phosphide, or galliumindium phosphide. The substrate 1302 may be substantially similar to thesubstrate 502 in FIGS. 5 and 8-9, and/or the substrate 1002 in FIG. 10.

The lower wafer 1300 includes four main functional areas: a fluidiccontrol circuitry area, a solid-state based photosensor array area, alogic circuitry area, and a microfluidic channel area. The circuitry andphotosensor array areas are formed in the substrate 1302 and/or in aninter-metal dielectric (IMD) layer 1304 formed on the substrate 1302.The IMD layer 1304 may be formed using any suitable deposition method,such as CVD, PVD, or ALD. The IMD layer 1304 may also be formed using aspin-coating process.

Still referring to FIG. 13A, the fluidic control circuitry area includesfluidic control circuitry 1306, which includes a plurality ofmetallization layer connected with associated transistors and othercircuit components. The sensor array area includes a photosensor array1308 and photosensor control circuitry 1310. The photosensor array 1308may be an array of transistor-based photosensors and is a CMOS imagesensor array. However, in other embodiments the photosensor array mayinclude photodiodes, active pixel sensors, phototransistors,photoresistors, charged coupled devices, or the like. The photosensorarray 1308 is controlled by the photosensor control circuitry 1310,which also includes a plurality of transistors and other circuitcomponents. Finally, in the logic circuitry area, there is a significantamount of logic circuitry 1312 including transistors and other circuitcomponents. The logic circuitry 1312 allows for input to and output fromthe lower wafer 1302. Further logic circuitry 1312 is coupled to boththe photosensor control circuitry 1310 and the fluidic control circuitry1306, to provide both with signal processing for optimal operation, suchas analog-to-digital and digital-to-analog conversion. Fluidic controlcircuitry 1306, photosensor control circuitry 1310, and logic circuitry1312 are embedded in the IMD layer 1304. In some embodiments, the lowerportion 1202 of the lower wafer 1200 in FIGS. 12A-12B may besubstantially similar to the wafer 1302, the fluidic control circuitryarea, the sensor array area, and the logic circuitry area in the lowerwafer 1300 in FIGS. 13A-13E. The IMD layer 1304, the fluidic controlcircuitry area, the solid-state based photosensor array area, and thelogic circuitry area may be substantially similar to the correspondingcomponents as discussed in FIGS. 5 and 8-10.

As shown in FIG. 13A, a metal layer 1320 is formed on the IMD layer1304. The metal layer 1320 may include aluminum copper alloy (AlCu) orcopper (Cu). The metal layer 1320 may also include any other suitablematerials that can be used for the electrodes of the microfluidicbio-entity manipulation and processing system. The metal layer 1320 maybe deposited using a sputtering process or an electroplating process.One or more other suitable deposition processes, such as CVD, or ALD mayalso be used for forming the metal layer 1320. The thickness of themetal layer 1320 is in a range from about 2 μm to about 100 μm.

Referring to FIG. 13B, one or more vertical electrodes 1322 are formedin the metal layer 1320 using a lithography process and an etchingprocess. The lithography process may include forming a photoresist layer(resist) overlying the metal layer 1320, exposing the resist to apattern, performing a post-exposure bake process, and developing theresist to form masking elements including the resist. The maskingelements may be used in the lithography process for patterning the metallayer 1320 to define the dimension and the layout of the verticalelectrodes 1322. The metal layer 1320 may then be recessed using themasking elements by any appropriate dry etching and/or wet etchingmethods. The recessing process may include a dry etching process, a wetetching process, or combinations thereof. For example, the metal layer1320 may be etched using a reactive-ion etching (RIE) process. Themasking elements may then be removed from the vertical electrodes 1322using a suitable etching process, such as a wet stripping process, aplasma ashing process, or any other suitable methods. In someembodiments, the vertical electrodes 1322 may be formed using a lift-offprocess.

In some embodiments, a damascene process may be used to form the one ormore vertical electrodes 1322. For example, during a damascene process,trenches and/or vias are formed in a dielectric material layer, copperor tungsten is then filled in the trenches and/or vias. A chemicalmechanical polishing (CMP) process is applied to remove excessive metalon the dielectric material layer and to planarize the top surface.

As shown in FIG. 13B, in some embodiments, the width of the distance (w)between two adjacent vertical electrodes or the width (w) of themicrofluidic channel is in a range from about 30 μm to about 1000 μm.The vertical electrodes 1322 in FIGS. 13B-13E may be substantiallysimilar to the vertical electrodes 1210 in FIGS. 12A-12B.

It is to be understood that the three depicted vertical electrodes areexemplary, any number of vertical electrodes may be included in themicrofluidic bio-entity manipulation and processing system. In someembodiments, one or more vertical electrodes are in communication withthe fluidic control circuitry 1306, and thus may be in an ON or OFFstate as described in connection with FIG. 3.

Referring to FIG. 13C, a dielectric layer 1328 is deposited on the oneor more vertical electrodes 1322. As shown in FIG. 13C, the dielectriclayer 1328 is formed to conform to the surface of the verticalelectrodes 1322. In some embodiments, the dielectric layer 1328 is ahigh-k dielectric layer formed by an atomic layer deposition (ALD)process, or a chemical vapor deposition (CVD) process, then followed byan annealing process. The dielectric layer 1328 includes one or morematerials selected from the group consisting of silicon oxide, siliconnitride, aluminum oxide, tantalum oxide, hafnium oxide, and bariumstrontium titanate. In some examples, the dielectric layer 1328 includesone or more materials selected from the group consisting of SiO2, Si3N4,Al2O3, Ta2O5, HfO, and (Ba, Sr)TiO3. In some embodiments, the dielectricconstant of the materials in the dielectric layer 1328 is in a rangefrom about 4 to about 800. The thickness of the dielectric layer 1328 isin a range from about 100 Å to about 1 μm. The dielectric layer 1328 inFIGS. 13C-13E may be substantially similar to the dielectric layer 1232in FIGS. 12A-12B.

Referring to FIG. 13D, a hydrophobic coating 1330 is formed on thedielectric layer 1328. The hydrophobic coating 1330 is also formed toconform to the surface of the vertical electrodes 1322 and thedielectric layer 1232. In some embodiments, the hydrophobic coating 1330is made from polytetrafluoroethylene (PTFE), while in other embodimentsit is a self-assembled monolayer. The hydrophobic coating 1330 may beformed using a spin-coating process or any other suitable methods. Thethickness of the hydrophobic coating 1330 is in a range from about 10 Åto about 1 μm. The hydrophobic coating 1330 in FIGS. 13D-13E may besubstantially similar to the dielectric layer 1234 in FIGS. 12A-12B.

Referring to FIG. 13E, a trench 1332 is formed using a suitable etchingprocess to reveal a contact pad 1334. The trench 1332 may be formed byetching through a portion of the hydrophobic coating 1330, a portion ofthe dielectric layer 1328, and a thickness of the IMD 1304 to expose anupper surface of the contact pad 1334. The contact pad 1334 may beprovided to allow power or ground to be supplied to the lower wafer1300, or to allow for signal/control input or output. The contact pad1334 and the process of forming thereof in FIG. 13E may be substantiallysimilar to that of FIG. 5.

FIG. 14 is a flowchart of a method 1400 for forming vertical electrodes1322 in a microfluidic bio-entity manipulation and processing systemaccording to some embodiments of the present disclosure. It should beunderstood that additional processes may be provided before, during, andafter the method 1400 of FIG. 14, and that some other processes may bebriefly described herein. To better illustrate method 1400 in operation,reference will be made to the lower wafer 1300 as discussed in FIGS.13A-13E. It is to be understood that reference to FIGS. 13A-13E are notsupposed to be limiting, and the method 1400 may also be explained withreference to other embodiments of the microfluidic bio-entitymanipulation and processing systems in the present disclosure.

Method 1400 starts from a process 1402 by forming a metal layer 1320 onan inter-metal (IMD) layer 1304. The IMD layer 1304 is formed on thesubstrate 1302, and the IMD layer 1304 includes one or more circuitries.The metal layer 1320, the IMD layer 1304 and the substrate 1302 areprovided a lower wafer, e.g., the lower wafer 1300. The lower wafer mayinclude one or more functional areas, such as a fluidic controlcircuitry area, a solid-state based photosensor array area, a logiccircuitry area, and a microfluidic channel area as shown in FIGS.13A-13E. The circuitry and photosensor array areas may be formed in thesubstrate 1302 and/or in the inter-metal dielectric layer (IMD) 1304.

Method 1400 proceeds to a process 1404 by patterning the metal layer(e.g., the metal layer 1320 ) to form one or more vertical electrodes(e.g., the vertical electrodes 1322). The one or more verticalelectrodes may be formed using a lithography process and an etchingprocess. One or more masking elements may be used in the lithographyprocess for patterning the metal layer to define the dimension and thelayout of the vertical electrodes. The metal layer may then be recessedusing the masking elements by any appropriate dry etching and/or wetetching methods, e.g., a RIE process, or a lift-off process. In somealternative embodiments, the one or more vertical electrodes may beformed using a damascene process.

Method 1400 proceeds to a process 1406 by depositing a dielectric layer(e.g., the dielectric layer 1328 ) on the one or more verticalelectrodes 1322. As shown in FIG. 13C, the dielectric layer 1328 isformed to conform to the surface of the vertical electrodes 1322. Insome embodiments, the dielectric layer 1328 is a high-k dielectric layerformed by an atomic layer deposition (ALD) process, or a chemical vapordeposition (CVD) process, then followed by an annealing process.

Method 1400 proceeds to a process 1408 by forming a hydrophobic coating(e.g., the hydrophobic coating 1330) on the dielectric layer. Thehydrophobic coating 1330 may be formed using a spin-coating process orany other suitable methods.

Method 1400 proceeds to a process 1410 by forming a trench (e.g., thetrench 1332) to expose a contact pad (e.g., the contact pad 1334). Thetrench may be formed using a suitable etching process to reveal thecontact pad. The trench 1332 may be formed by etching through a portionof the hydrophobic coating 1330, a portion of the dielectric layer 1328,and a thickness of the IMD 1304 to expose an upper surface of thecontact pad 1334 as shown in FIG. 13E.

As disclosed with reference to FIGS. 13A-13E and 14, a patterningprocess including a lithography process and an etching process may beused to define and form the one or more vertical electrodes on thesubstrate. The lithography process may be used to define themicrofluidic channel formed between two vertical electrodes. The presentdisclosure may provide improved control and more flexibility in tuningthe widths of the channel gaps. For example, the microfluidic channelswith various widths of channel gaps as shown in FIG. 12C may be formedusing the patterning process as disclosed in the present disclosure.

FIG. 15A is a cross-sectional diagram of a microfluidic bio-entitymanipulation and processing system 1500 according to some embodiments ofthe present disclosure. As shown in FIG. 15A, the microfluidicbio-entity manipulation and processing system 1500 includes a lowerwafer 1300 as fabricated in FIGS. 13A-13E, and an upper wafer 1502. Themicrofluidic bio-entity manipulation and processing system 1500 mayinclude the vertical electrodes in the present disclosure fortransporting and mixing target bio-entities as discussed with referenceto FIG. 4. Actions like those described in connection with FIG. 3 may beused to move, split, merge, and form droplets.

FIG. 15B is a cross-sectional diagram of an upper wafer 1502 that may beused in a bio-entity manipulation and processing system 1500. As shownin FIG. 15B, the upper wafer 1502 may include a substrate 1504 and ahydrophobic coating 1506 formed on the substrate. One or more labelingareas 1508 may be formed in the hydrophobic coating 1506.

Referring back to FIG. 15A, in some embodiments, the upper wafer 1502may be in direct contact with the one or more vertical electrodes 1322of the lower wafer 1300. In some alternative embodiments, the upperwafer 1502 may not be in direct contact with the lower wafer 1300. Inthe present embodiments, a voltage may not be needed to apply to theupper 1502. The electric fields may be applied onto various verticalelectrodes in the lower wafer to manipulate the transporting process ofthe microfluidic droplets.

A bio-entity droplet (e.g., bio-entity droplet 1326 and/or bio-entitydroplet 1327) including DNA, antibody and/or protein may be filled inthe microfluidic channel formed between adjacent vertical electrodes onthe lower wafer 1300. The bio-entity droplet may be brought into contactwith the labeling areas 1508 on the upper wafer 1502 for a chemicalreaction generating photonic emission. In some embodiments, thecolorimetric analysis (e.g., colorimetric determination of glucose), orfluorescent reaction may be implemented into the microfluidic bio-entitymanipulation and processing system 1500. The bio-entity droplet may belabeled on bead (e.g., made by gold, polystyrene, magnetic beads whichmay be controlled by the droplet/microfluidic circuitry.)

For example, referring again to FIG. 4, during the sample preparation,some bio-entity (DNA, antibody, protein) is labeled on the bead (e.g.,made by gold, polystyrene, magnetic bead). Afterward, the sample beadscould be loaded on the sample tank 410A-410D. By utilizing thedroplet/microfluidic circuitry, the bio-sample beads could be carried bythe droplet movement from the sample tank and mixed with the reagent toperform the bio-reaction. Then, the photosensors could detect thereaction. In this example, the “sample preparation” is another stepbefore loading fluidic on to the chip.

The contact between the labeling area 1508 and the bio-entity sampledroplet 1326 may undergo a chemical reaction which intensifies orenhances the fluorescent light signal. This light passes to thephotosensor array 1308 to be detected and a corresponding signal is sentto the logic circuitry 1312 for processing. Logic circuitry 1312 mayinterpret the signal by color or frequency to determine the biochemicalreaction that occurred. The biochemical reaction may indicate that aspecific base nucleotide was detected in a target DNA fragment, or thata particular antibody was present in the bio-entity sample droplet.After the bio-entity sample droplet 1326 has been processed, it may beremoved from the microfluidic channel.

In some examples, the droplet 1326 may include a tagged bio-entitysample, such as DNA mixed with a reagent droplet such as the exemplaryadenine reagent droplet 408B from FIG. 4 or FIG. 16. When the droplet1326 contacts the labeling area 1508, chemical reactions may remove thetag from the bio-entity samples in the droplet 1326. The removal of thetag may enhance or intensify a photonic emission. The photonic emissionmay be sensed by the photosensor array 1308. This signal is captured bythe photosensor control circuitry 1310, and transmitted to the logiccircuitry 1312 for signal processing. Depending on the frequency orcolor of the photonic emission, a specific base pair may be detected.

In some other examples, antibodies in the droplet 1327 are being tested.When the droplet 1327 contacts the labeling area 1508 of the upper wafer1502, reactions between the droplet 1327 and the labeling area 1508 mayresult in a photonic emission, which indicates the presence of theparticular antibody in the bio-entity sample in droplet 1327.

FIG. 16 is an illustrative top view of an integrated microfluidicbio-entity manipulation and processing device 1600 according to someembodiments of the present disclosure. For the clarity of thediscussion, FIG. 16 is discussed as below in reference with FIG. 15A.However, this should not be understood as limiting such features. Insome embodiments, one or more of the vertical paths 402A-J and each ofhorizontal paths 404A-L of the microfluidic grid 400 may be formed fromthe one or more microfluidic channels formed among a plurality ofvertical electrodes as discussed in FIGS. 12A-12C, and fabricated usingthe processes as discussed in FIGS. 13A- 13E and 14.

Referring to FIG. 16, the logic circuitry area may include one or morecircuitries for the sensor array controller, fluidic path controlprogram, clock, D/A converter, A/D converter, and the wireless dataoutput. The device 1600 also includes the contact pad 1334 for providingpower supply, and/or signal input/output.

Referring to FIG. 16, a sensor array area of the device 1600 includes amicrofluidic grid 400 which may be substantially similar to themicrofluidic grid 400 as discussed in FIG. 4. The microfluidic grid 400includes one or more reagent tanks for storing reagents, and one or moresamples tanks for storing the bio-entity samples. The reagents may bemixed with the sample droplets for tagging the droplets before thedroplets are brought in contact with the labeling areas 1508 of theupper wafer. As shown in FIG. 16, each of the square areas 410 mayrepresent a target DNA fragment, such as exemplary target DNA fragment410, that can be manipulated as described above in connection with FIG.3 for various operations, such as the lateral movement 300A, the dropletsplit 300B, the droplet merger 300C, and the droplet formation 300D. Thearea underneath the microfluidic grid 400 includes an image sensorarray, which may be used to detect photonic signals and to takelight-based measurements in order to sequence the target DNA fragmentsamples. The image sensor array may utilize a front-side illumination ora back-side illumination according to various embodiments of the presentdisclosure.

Still referring to FIG. 16, the fluidic control circuitry area mayinclude a droplet actuator array controller configured to manipulate thetransporting and mixing of each sample droplet. Each vertical electrodeas represented by the vertical and horizontal path of the microfluidicgrid 400 may be connected to the fluidic control circuitry.

Referring to FIGS. 15A and 16, the bio-entity sample droplet 1326 ismoved in the microfluidic channel formed between vertical electrodesusing the electrowetting effect. As discussed in FIG. 12A, bycontrolling the electrical fields, the droplet may be guided into mixingwith the reagent from the reagent tanks to be tagged before contactingthe labeling area 1508. The droplet in the microfluidic channel may alsobe guided into contact with the labeling area 1508. For example, asample droplet provided by sample tank 410B may be transported tocontact with a reagent droplet provided by reagent tank 406A at thesquare 1606, the mixed sample droplet is then brought into contact withthe labeling area 1508 for a chemical reaction to generate a photonicsignal to be detected by the image sensor array 1308. Guiding thebio-entity sample droplet into contact with the labeling area 1508 maybe accomplished by having the logic circuitry 1312 exert control overthe fluidic control circuitry 1306.

In some alternative embodiments, the photonic signals detected by theimage sensor may be generated by reactions between the bio-entitysamples provided by the sample tanks and the reagents provided by thereagent tanks in the microfluidic grid 400. For example, a sampledroplet provided by sample tank 410B may be transported to react with areagent droplet provided by reagent tank 406A at the square 1606, and aphotonic signal may be generated by the reaction and may be detected bythe image sensor. In addition, one could add the bead with sampleapproach in this embodiment.

FIG. 17 is a flowchart of a method 1700 for manipulating and processingbio-entity samples with a microfluidic bio-entity manipulation andprocessing system according to some embodiments of the presentdisclosure. The method 1700 begins in step 1702 by providing abio-entity sample droplet to a microfluidic channel. The bio-entitysample droplet may be obtained from one or more tanks coupled to amicrofluidic grid. In some examples, the method 1700 may also includemixing a bio-entity sample from a sample tank with a reagent from areagent tank of the microfluidic grid 400 to form a bio-entity samplefor testing. In an exemplary embodiment of the present disclosure asshown in FIG. 15A, the microfluidic channel is formed between twovertical electrodes on the lower wafer 1300.

The method 1700 proceeds to step 1704 by transporting the bio-entitysample droplet in the microfluidic channel using an electrowettingeffect by applying an electric field between the two verticalelectrodes. The microfluidic channel is formed between two verticalelectrodes on the lower wafer as discussed in FIGS. 13A-13E and 14. Whenin the microfluidic channel the bio-entity sample droplet may be broughtinto contact with a labeling area in the upper wafer. A biochemicalreaction is triggered upon contact between the bio-entity sample dropletand the labeling area.

The method 1700 then proceeds to step 1706 by detecting a photonicsignal produced by the interaction between the bio-entity sample dropletand the labeling area of the upper wafer. The photonic signal isdetected by a photosensor array that is embedded in the lower wafer.

The present embodiments describe structure and method for formingvertical electrodes on a lower wafer of a microfluidic bio-entitymanipulation and processing system. A microfluidic channel is formedbetween two adjacent vertical electrodes on the lower wafer fortransporting the bio-entity sample droplet. The photonic signalgenerated from the interaction between the bio-entity sample droplet andthe vertical electrodes may be detected using a photosensor array formedin the lower wafer. The mechanisms of the vertical electrodes mayprovide precise microfluidic channel gap control and simplifiedmanufacturing process. No external fluidic component, such as a pump, avalve, or a mixer, is necessary for the present disclosure. Themechanisms may also provide a flexible fluidic control, such as anaddressable fluidic path and/or a better fluidic resolution. Inaddition, less amount of the sample droplet or the reagent, e.g., asample droplet or a drop of reagent at pico liters levels, may be usedin the microfluidic bio-entity manipulation and processing systemincluding the vertical electrodes as discussed in the presentdisclosure. The various embodiments of the microfluidic bio-entitymanipulation and processing system in the present disclosure may includeintegrating transistor based light sensor and/or integrating ionsensitive field-effect transistor (ISFET). The integration capabilityprovided in the present disclosure may include various benefits, such ascapable of controlling sensor, microfluidic sample, and reagents usingelectrical signals; offering low cost of fluidic component; offeringCMOS compatible process; and potentials for realizing portable devicefor lab-on-a-chip (LOC) device.

The present disclosure provides a device for manipulating and processingbio-entity samples comprises a first microfluidic channel formed betweena first electrode and a second electrode and on a first substrate, thefirst microfluidic channel coupled to fluidic control circuitry; andlogic circuitry coupled to the fluidic control circuitry and a sensorcontrol circuitry. The first electrode and the second electrode areformed on the first substrate.

The present disclosure provides a method for fabricating a semiconductordevice for manipulating and processing microfluidic bio-entity samplescomprises forming a metal layer on an inter-metal dielectric (IMD) layerformed on a substrate, one or more circuitries being embedded in the IMDlayer; patterning the metal layer to form a first electrode and a secondelectrode, a first microfluidic channel being formed between the firstelectrode and the second electrode on the IMD layer; and depositing adielectric layer on the first electrode and the second electrode. Thedielectric layer is conformed to surface of the first electrode and thesecond electrode.

The present disclosure provides a method for manipulating and processingbio-entity samples with a semiconductor device comprises providing abio-entity sample droplet to a microfluidic channel formed between afirst electrode and a second electrode formed on a substrate;transporting the bio-entity sample droplet in the microfluidic channelusing an electrowetting effect by applying an electric field between thefirst electrode and the second electrode; and detecting a photonicsignal using a photosensor array. The photonic signal is generated by aninteraction between the bio-entity sample droplet and a labeling area onthe upper wafer.

The preceding disclosure is submitted by way of discussion and example.It does not exhaust the full scope and spirit of the disclosure andclaims. Such variations and combinations as may be apparent to one ofskill in the art are considered to be within the scope and spirit ofthis disclosure. For instance, throughout the disclosure, DNA sequencingis presented as an example, along with pathogen identification. Thescope and spirit of the disclosure extends well beyond the limitedcontext of these examples. Thus, the full extent of the disclosure islimited only by the following claims.

What is claimed is:
 1. A device for manipulating and processingbio-entity samples, the device comprising: a first microfluidic channelformed between a first electrode and a second electrode and on a firstsubstrate, the first microfluidic channel coupled to fluidic controlcircuitry; and logic circuitry coupled to the fluidic control circuitryand a sensor control circuitry, wherein the first electrode and thesecond electrode are formed on the first substrate.
 2. The device ofclaim 1, further comprising: a microfluidic grid formed on the firstsubstrate and including the first electrode, the second electrode, andthe first microfluidic channel; and a photosensor array coupled to thesensor control circuitry, wherein the microfluidic grid is coupled to afirst reservoir and a second reservoir, wherein the microfluidic grid isconfigured to transport a bio-entity sample by electrowetting, and tomix the bio-entity sample from the first reservoir with a reagent from asecond reservoir, and wherein the photosensor array is configured todetect a photonic signal.
 3. The device of claim 1, wherein the fluidiccontrol circuitry, the sensor control circuitry, and the logic circuitryare embedded in an inter-metal dielectric (IMD) layer formed on thefirst substrate, and wherein the first electrode and the secondelectrode are formed on the IMD layer.
 4. The device of claim 1, furthercomprising: a dielectric layer formed on each of the first electrode andthe second electrode, the dielectric layer being conformed to surface ofeach of the first electrode and the second electrode; and a hydrophobiccoating formed on the dielectric layer.
 5. The device of claim 4,wherein the dielectric layer includes one or more materials selectedfrom the group consisting of SiO2, Si3N4, Al2O3, Ta2O5, HfO, and (Ba,Sr)TiO3.
 6. The device of claim 4, wherein a thickness of the dielectriclayer is in a range from about 100 Å to about 1 μm.
 7. The device ofclaim 4, wherein a thickness of the hydrophobic coating is in a rangefrom about 10 Å to about 1 μm.
 8. The device of claim 4, furthercomprising a labeling area configured to interact with the bio-entitysample to generate a photonic signal to be detected by a photosensorarray coupled to the sensor control circuitry.
 9. The device of claim 1,wherein a width of the first microfluidic channel is in a range fromabout 30 μm to about 1000 μm.
 10. The device of claim 1, furthercomprising: a second microfluidic channel formed between a thirdelectrode and a fourth electrode, wherein the second microfluidicchannel, the third electrode, and the fourth electrode are formed on thefirst substrate, and wherein a width of the first microfluidic channelis different from a width of the second microfluidic channel.
 11. Thedevice of claim 1, wherein a height of each of the first electrode andthe second electrode is in a range from about 2 μm to about 100 μm. 12.The device of claim 1, wherein a length of each of the first electrodeand the second electrode is in a range from about 50 μm to about 1000μm.
 13. A method for fabricating a semiconductor device for manipulatingand processing microfluidic bio-entity samples, the method comprising:forming a metal layer on an inter-metal dielectric (IMD) layer formed ona substrate, one or more circuitries being embedded in the IMD layer;patterning the metal layer to form a first electrode and a secondelectrode, a first microfluidic channel being formed between the firstelectrode and the second electrode on the IMD layer; and depositing adielectric layer on the first electrode and the second electrode, thedielectric layer being conformed to surface of the first electrode andthe second electrode.
 14. The method of claim 13, further comprising:forming a hydrophobic coating on the dielectric layer.
 15. The method ofclaim 13, wherein the patterning the metal layer includes: performing alithography process to the metal layer to form one or more maskingelements; and etching the metal layer using the one or more maskingelements to form the first electrode and the second electrode on the IMDlayer.
 16. The method of claim 15, wherein the etching the metal layerfurther comprises: etching the metal layer to form a third electrode anda fourth electrode on the IMD layer, wherein a second microfluidicchannel is formed between the third electrode and the fourth electrode,and wherein a width of the first microfluidic channel is different froma width of the second microfluidic channel.
 17. The method of claim 13,wherein depositing the dielectric layer includes depositing thedielectric layer on and conformed to the surface of the first electrodeand the second electrode using one or more methods selected from thegroup consisting of an atomic layer deposition (ALD) process and achemical vapor deposition (CVD) process.
 18. The method of claim 13,further comprising: forming a trench to expose a contact pad embedded inthe IMD layer.
 19. A method for manipulating and processing bio-entitysamples with a semiconductor device, the method comprising: providing abio-entity sample droplet to a microfluidic channel formed between afirst electrode and a second electrode formed on a substrate;transporting the bio-entity sample droplet in the microfluidic channelusing an electrowetting effect by applying an electric field between thefirst electrode and the second electrode; and detecting a photonicsignal using a photosensor array, wherein the photonic signal isgenerated by an interaction between the bio-entity sample droplet and alabeling area.
 20. The method of claim 19, further comprising: mixingthe bio-entity sample droplet with a reagent droplet, wherein thephotonic signal is generated by a reaction between the bio-entity sampledroplet and the reagent droplet.